A primary function of the brain is to store and retrieve information. Except for working memory, where extracellular recordings demonstrate persistent discharges during delay-response tasks, it has been difficult to link memories with changes in individual neurons or specific synaptic connections. Here, we demonstrate that transient stimuli are reliably encoded in the ongoing activity of brain tissue in vitro. We found that the patterns of synaptic input onto dentate hilar neurons predict which of four pathways were stimulated with an accuracy of 76% and performed significantly better than chance for >15 s. Dentate gyrus neurons also could accurately encode temporal sequences using population representations that were robust to variation in sequence interval. These results demonstrate direct neural encoding of temporal sequences in the spontaneous activity of brain tissue and suggest a novel local circuit mechanism that may contribute to diverse forms of short-term memory.